Started Running as brainvisa ================================================================================ ---------------------------------------- $ /usr/bin/python3 /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=brainvisa-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/ref -- sh -c '/casa/install/bin/bv_env_test "timeout" "-k" "10" "1800" "vip_test_well_composed_configurations"' ---------------------------------------- ================================================================================ SUCCESS (exit code 0) ================================================================================ ---------------------------------------- $ /usr/bin/python3 /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=brainvisa-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/ref -- sh -c '/casa/install/bin/bv_env_test "timeout" "-k" "10" "1800" "vip_test_well_composed_topology"' ---------------------------------------- ================================================================================ SUCCESS (exit code 0) ================================================================================ ---------------------------------------- $ /usr/bin/python3 /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=brainvisa-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/ref -- sh -c '/casa/install/bin/bv_env_test "timeout" "-k" "10" "5400" "python3" "-m" "brainvisa.tests.test_morphologist" "--no-ann" "--test_mode=run"' ---------------------------------------- ['/casa/install/python/brainvisa/tests/test_morphologist.py', '--no-ann', '--test_mode=run'] Starting tests under /tmp/axon_test_hlmw19is Loading toolbox brainrat Loading toolbox cortical_surface Loading toolbox data management Loading toolbox freesurfer Loading toolbox highres_cortex Loading toolbox morphologist Loading toolbox primatologist Loading toolbox spm Loading toolbox structural_analysis Loading toolbox tools Loading toolbox viewers Loading toolbox My processes The log file for this session is '/tmp/axon_test_hlmw19is/bv_home/brainvisa.log' exec: /casa/install/brainvisa/toolboxes/morphologist/startup.py SPM dir: /usr/local/spm12-standalone spmtemplates: /usr/local/spm12-standalone/spm12_mcr/spm12/spm12 /usr/local/spm12-standalone/spm12_mcr/spm12/spm12: parse directories and insert items /usr/local/spm12-standalone/spm12_mcr/spm12/spm12: 8 files are stored as 8 DiskItems in 0 seconds test_pipeline_results (__main__.TestMorphologistPipeline) ... Database /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/ref/test_morphologist_pipeline/db_morphologist must be updated because the database file is too old. Generating database tables for /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/ref/test_morphologist_pipeline/db_morphologist /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/ref/test_morphologist_pipeline/db_morphologist: parse directories and insert items /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/ref/test_morphologist_pipeline/db_morphologist: 188 files are stored as 182 DiskItems in 0 seconds * Create test database /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist: parse directories and insert items /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist: 2 files are stored as 2 DiskItems in 0 seconds Generating database tables for /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist: parse directories and insert items /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist: 2 files are stored as 2 DiskItems in 0 seconds * Download https://brainvisa.info/download/data/demo_data.zip to /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline * Import test data _Process **Import T1 MRI** started on 2025/07/28 04:14_ filein : /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/data_unprocessed/sujet01/anatomy/sujet01.ima fileout : /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/sujet01.nii encoding: Binary normal : 0 rescale : 0 format : type : S16 objtype : xdim : 0 ydim : 0 zdim : 0 imin : default imax : default omin : default omax : default reading /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/data_unprocessed/sujet01/anatomy/sujet01.ima as Volume / S16... reading done convert to Volume / S16 converting data... convert done writing /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/sujet01.nii... done _Process **Import T1 MRI** finished on 2025/07/28 04:14 (2 seconds)_ (not doing ANN sulci recognition tests today) * Check SPAM models installation _Process **Check SPAM models installation** started on 2025/07/28 04:14_ models: 6 SPAM models are present. _Process **Check SPAM models installation** finished on 2025/07/28 04:14 (0 seconds)_ * Run Morphologist _Process **Morphologist 2021** started on 2025/07/28 04:14_ progress: 0.0 % ... progress: 0.0 % ... WARNING: Left hemisphere point not specified - X axis flip will not be checked --- OK, the image seems to be in the correct orientation. progress: 10.0 % ... progress: 10.0 % ... progress: 20.0 % ... progress: 30.0 % ... progress: 40.0 % ... Skip unselected node: Skull-stripped brain normalization progress: 50.0 % ... progress: 60.0 % ... progress: 70.0 % ... progress: 80.0 % ... progress: 80.0 % ... progress: 80.0 % ... Computing left hemisphere grey-white classification... progress: 80.71428571428572 % ... Detecting left hemisphere spherical inner cortical interface... progress: 81.42857142857143 % ... Reconstructing left hemisphere white mesh... progress: 82.14285714285714 % ... Computing left sulci skeleton and buried gyrus watershed... progress: 82.85714285714286 % ... Detecting left hemisphere spherical outer cortical surface... Reconstructing left hemisphere pial mesh... progress: 83.57142857142857 % ... Building left hemisphere attributed relational sulci graph... _Process **Hemisphere Sulci Voronoi** started on 2025/07/28 04:17_ _Process **Hemisphere Sulci Voronoi** finished on 2025/07/28 04:17 (26 seconds)_ _Process **Hemisphere Sulci Thickness and Volumes** started on 2025/07/28 04:17_ _Process **Hemisphere Sulci Thickness and Volumes** finished on 2025/07/28 04:17 (18 seconds)_ Talairach-AC/PC-Anatomist appended progress: 84.28571428571429 % ... progress: 84.28571428571429 % ... progress: 84.28571428571429 % ... progress: 84.64285714285712 % ... progress: 84.64285714285712 % ... progress: 85.0 % ... progress: 85.0 % ... progress: 85.0 % ... progress: 85.0 % ... progress: 85.0 % ... progress: 85.0 % ... Computing right hemisphere grey-white classification... progress: 85.71428571428571 % ... Detecting right hemisphere spherical inner cortical interface... progress: 86.42857142857142 % ... Reconstructing right hemisphere white mesh... progress: 87.14285714285714 % ... Computing right sulci skeleton and buried gyrus watershed... progress: 87.85714285714286 % ... Detecting right hemisphere spherical outer cortical surface... Reconstructing right hemisphere pial mesh... progress: 88.57142857142858 % ... Building right hemisphere attributed relational sulci graph... _Process **Hemisphere Sulci Voronoi** started on 2025/07/28 04:23_ _Process **Hemisphere Sulci Voronoi** finished on 2025/07/28 04:23 (25 seconds)_ _Process **Hemisphere Sulci Thickness and Volumes** started on 2025/07/28 04:23_ _Process **Hemisphere Sulci Thickness and Volumes** finished on 2025/07/28 04:24 (17 seconds)_ Talairach-AC/PC-Anatomist appended progress: 89.28571428571429 % ... progress: 89.28571428571429 % ... progress: 89.28571428571429 % ... progress: 89.64285714285714 % ... progress: 89.64285714285714 % ... progress: 90.0 % ... progress: 90.0 % ... progress: 90.0 % ... progress: 90.0 % ... progress: 90.0 % ... progress: 90.0 % ... Reading FGraph version 3.1 Reading FGraph version 3.1 progress: 100.0 % ... _Process **Morphologist 2021** finished on 2025/07/28 04:28 (13 minutes 55 seconds)_ * Run CNN recognition _Process **Morphologist 2021** started on 2025/07/28 04:28_ progress: 0.0 % ... Skip unselected node: Image orientation handling progress: 10.0 % ... Skip unselected node: T1 Bias Correction progress: 20.0 % ... Skip unselected node: Histogram analysis progress: 30.0 % ... Skip unselected node: Compute Brain Mask progress: 40.0 % ... Skip unselected node: Skull-stripped brain normalization progress: 50.0 % ... Skip unselected node: Split Brain Mask progress: 60.0 % ... Skip unselected node: Talairach transformation from manual AC/PC progress: 70.0 % ... Skip unselected node: Head Mesh progress: 80.0 % ... progress: 80.0 % ... progress: 80.0 % ... Skip unselected node: Grey White Classification progress: 80.71428571428572 % ... Skip unselected node: Grey White Topology Correction progress: 81.42857142857143 % ... Skip unselected node: Grey White Mesh progress: 82.14285714285714 % ... Skip unselected node: Sulci Skeleton and Roots progress: 82.85714285714286 % ... Skip unselected node: Pial Mesh progress: 83.57142857142857 % ... Skip unselected node: Cortical Folds Graph progress: 84.28571428571429 % ... progress: 84.28571428571429 % ... CONFIG: {'capsul_engine': {'uses': {'capsul.engine.module.freesurfer': 'ALL', 'capsul.engine.module.fom': 'ALL', 'capsul.engine.module.attributes': 'any', 'capsul.engine.module.axon': 'any', 'capsul.engine.module.spm': 'ALL', 'capsul.engine.module.matlab': 'any', 'capsul.engine.module.fsl': 'ALL', 'capsul.engine.module.ants': 'ALL', 'capsul.engine.module.afni': 'ALL'}}, 'capsul.engine.module.fom': {'config_id': 'fom', 'config_environment': 'global', 'input_fom': 'morpho-deepsulci-1.0', 'output_fom': 'morpho-deepsulci-1.0', 'shared_fom': 'raw-bids-1.0', 'volumes_format': 'gz compressed NIFTI-1 image', 'meshes_format': 'GIFTI file', 'auto_fom': True, 'fom_path': [], 'input_directory': '/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist', 'output_directory': '/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist'}, 'capsul.engine.module.attributes': {'config_id': 'attributes', 'config_environment': 'global', 'attributes_schema_paths': ['capsul.attributes.completion_engine_factory'], 'attributes_schemas': {}, 'process_completion': 'builtin'}, 'capsul.engine.module.axon': {'config_id': 'axon', 'config_environment': 'global', 'shared_directory': '/casa/install/share/brainvisa-share-5.1', 'user_level': 0}, 'capsul.engine.module.spm': {'config_id': 'spm12-standalone', 'config_environment': 'global', 'directory': '/usr/local/spm12-standalone', 'version': '12', 'standalone': True}, 'capsul.engine.module.matlab': {'config_id': 'matlab', 'config_environment': 'global', 'mcr_directory': '/usr/local/spm12-standalone/mcr/v97'}} soma-workflow starting in light mode Workflow controller initialised Soma-workflow temp directory: /tmp/axon_test_hlmw19is/tmp/soma_workflow_bz5g5zc3 del WorkflowController progress: 85.0 % ... UUID conflict in database, uuid: 20b8864a-1d68-f989-de0f-a435cca6fcbb while inserting: test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/cnn_auto/Lsujet01_cnn_auto.arg file(s) with the same UUID: ('test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/Lsujet01.arg',) ('test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/Lsujet01.data',) error: UNIQUE constraint failed: _DISKITEMS_._uuid ERROR: ** brainvisa.data.sqlFSODatabase.DatabaseError: Cannot insert"/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/cnn_auto/Lsujet01_cnn_auto.arg" because its uuid is in conflict with the uuid of another file in the database. ** * * * `**DatabaseError**` Traceback (most recent call last): File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 1266, in insertDiskItems cursor.execute( sqlite3.IntegrityError: UNIQUE constraint failed: _DISKITEMS_._uuid During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/casa/install/python/brainvisa/processes.py", line 3500, in _processExecution neuroHierarchy.databases.insertDiskItem( File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 256, in insertDiskItem self.insertDiskItems((item, ), **kwargs) File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 2249, in insertDiskItems database.insertDiskItems((diskItem,), update=update, File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 1307, in insertDiskItems raise DatabaseError( brainvisa.data.sqlFSODatabase.DatabaseError: Cannot insert "/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/cnn_auto/Lsujet01_cnn_auto.arg" because its uuid is in conflict with the uuid of another file in the database. progress: 85.0 % ... progress: 85.0 % ... progress: 85.0 % ... Skip unselected node: Grey White Classification progress: 85.71428571428571 % ... Skip unselected node: Grey White Topology Correction progress: 86.42857142857142 % ... Skip unselected node: Grey White Mesh progress: 87.14285714285714 % ... Skip unselected node: Sulci Skeleton and Roots progress: 87.85714285714286 % ... Skip unselected node: Pial Mesh progress: 88.57142857142858 % ... Skip unselected node: Cortical Folds Graph progress: 89.28571428571429 % ... progress: 89.28571428571429 % ... CONFIG: {'capsul_engine': {'uses': {'capsul.engine.module.freesurfer': 'ALL', 'capsul.engine.module.fom': 'ALL', 'capsul.engine.module.attributes': 'any', 'capsul.engine.module.axon': 'any', 'capsul.engine.module.spm': 'ALL', 'capsul.engine.module.matlab': 'any', 'capsul.engine.module.fsl': 'ALL', 'capsul.engine.module.ants': 'ALL', 'capsul.engine.module.afni': 'ALL'}}, 'capsul.engine.module.fom': {'config_id': 'fom', 'config_environment': 'global', 'input_fom': 'morpho-deepsulci-1.0', 'output_fom': 'morpho-deepsulci-1.0', 'shared_fom': 'raw-bids-1.0', 'volumes_format': 'gz compressed NIFTI-1 image', 'meshes_format': 'GIFTI file', 'auto_fom': True, 'fom_path': [], 'input_directory': '/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist', 'output_directory': '/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist'}, 'capsul.engine.module.attributes': {'config_id': 'attributes', 'config_environment': 'global', 'attributes_schema_paths': ['capsul.attributes.completion_engine_factory'], 'attributes_schemas': {}, 'process_completion': 'builtin'}, 'capsul.engine.module.axon': {'config_id': 'axon', 'config_environment': 'global', 'shared_directory': '/casa/install/share/brainvisa-share-5.1', 'user_level': 0}, 'capsul.engine.module.spm': {'config_id': 'spm12-standalone', 'config_environment': 'global', 'directory': '/usr/local/spm12-standalone', 'version': '12', 'standalone': True}, 'capsul.engine.module.matlab': {'config_id': 'matlab', 'config_environment': 'global', 'mcr_directory': '/usr/local/spm12-standalone/mcr/v97'}} soma-workflow starting in light mode Workflow controller initialised Soma-workflow temp directory: /tmp/axon_test_hlmw19is/tmp/soma_workflow_hlrss1q1 del WorkflowController progress: 90.0 % ... UUID conflict in database, uuid: dc80ebf2-bac6-e663-f243-0cbad073d40e while inserting: test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/cnn_auto/Rsujet01_cnn_auto.arg file(s) with the same UUID: ('test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/Rsujet01.arg',) ('test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/Rsujet01.data',) error: UNIQUE constraint failed: _DISKITEMS_._uuid ERROR: ** brainvisa.data.sqlFSODatabase.DatabaseError: Cannot insert"/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/cnn_auto/Rsujet01_cnn_auto.arg" because its uuid is in conflict with the uuid of another file in the database. ** * * * `**DatabaseError**` Traceback (most recent call last): File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 1266, in insertDiskItems cursor.execute( sqlite3.IntegrityError: UNIQUE constraint failed: _DISKITEMS_._uuid During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/casa/install/python/brainvisa/processes.py", line 3500, in _processExecution neuroHierarchy.databases.insertDiskItem( File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 256, in insertDiskItem self.insertDiskItems((item, ), **kwargs) File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 2249, in insertDiskItems database.insertDiskItems((diskItem,), update=update, File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 1307, in insertDiskItems raise DatabaseError( brainvisa.data.sqlFSODatabase.DatabaseError: Cannot insert "/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/cnn_auto/Rsujet01_cnn_auto.arg" because its uuid is in conflict with the uuid of another file in the database. progress: 90.0 % ... progress: 90.0 % ... progress: 90.0 % ... Reading FGraph version 3.3 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.1 Warning: wrong filename_base in graph, trying to fix it progress: 100.0 % ... _Process **Morphologist 2021** finished on 2025/07/28 04:30 (1 minutes 48 seconds)_ Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.1 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.3 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.3 Warning: wrong filename_base in graph, trying to fix it ok ---------------------------------------------------------------------- Ran 1 test in 1196.998s OK RETURNCODE: True Exception ignored in: <function TemporaryDirectory.__del__ at 0x739dc199c700> Traceback (most recent call last): File "/casa/install/python/brainvisa/data/neuroDiskItems.py", line 2699, in __del__ TypeError: 'NoneType' object is not callable ================================================================================ SUCCESS (exit code 0) ================================================================================ ---------------------------------------- $ /usr/bin/python3 /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=brainvisa-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/ref -- sh -c '/casa/install/bin/bv_env_test "timeout" "-k" "10" "5400" "python3" "-m" "morphologist.tests.test_morphologist_capsul"' ---------------------------------------- ['/casa/install/python/morphologist/tests/test_morphologist_capsul.py'] Starting tests under /tmp/axon_test_qz0fz4xi Loading toolbox brainrat Loading toolbox cortical_surface Loading toolbox data management Loading toolbox freesurfer Loading toolbox highres_cortex Loading toolbox morphologist Loading toolbox primatologist Loading toolbox spm Loading toolbox structural_analysis Loading toolbox tools Loading toolbox viewers Loading toolbox My processes The log file for this session is '/tmp/axon_test_qz0fz4xi/bv_home/brainvisa.log' exec: /casa/install/brainvisa/toolboxes/morphologist/startup.py SPM dir: /usr/local/spm12-standalone spmtemplates: /usr/local/spm12-standalone/spm12_mcr/spm12/spm12 /usr/local/spm12-standalone/spm12_mcr/spm12/spm12: parse directories and insert items /usr/local/spm12-standalone/spm12_mcr/spm12/spm12: 8 files are stored as 8 DiskItems in 0 seconds test_pipeline_results (__main__.TestMorphologistCapsul) ... * Check SPAM models installation _Process **Check SPAM models installation** started on 2025/07/28 04:33_ models: 6 SPAM models are present. _Process **Check SPAM models installation** finished on 2025/07/28 04:33 (0 seconds)_ * Create test database /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist: parse directories and insert items /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist: 2 files are stored as 2 DiskItems in 0 seconds Generating database tables for /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist: parse directories and insert items /volatile/a-sac-ns-brainvisa/bbi- nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist: 2 files are stored as 2 DiskItems in 0 seconds * Download https://brainvisa.info/download/data/demo_data.zip to /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul * Import test data _Process **Import T1 MRI** started on 2025/07/28 04:34_ filein : /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/data_unprocessed/sujet01/anatomy/sujet01.ima fileout : /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist/test/sujet01/t1mri/default_acquisition/sujet01.nii encoding: Binary normal : 0 rescale : 0 format : type : S16 objtype : xdim : 0 ydim : 0 zdim : 0 imin : default imax : default omin : default omax : default reading /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/data_unprocessed/sujet01/anatomy/sujet01.ima as Volume / S16... reading done convert to Volume / S16 converting data... convert done writing /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist/test/sujet01/t1mri/default_acquisition/sujet01.nii... done _Process **Import T1 MRI** finished on 2025/07/28 04:34 (2 seconds)_ * create process Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' * Run Morphologist_Capsul to get test results _Process **Morphologist CAPSUL iteration** started on 2025/07/28 04:34_ Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' progress: 0.0 % ... Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' progress: 100.0 % ... jobs: 26 real, 26 total including barriers _Process **Morphologist CAPSUL iteration** finished on 2025/07/28 04:34 (2 seconds)_ workflow: /tmp/axon_test_qz0fz4xi/tmp/bv_xq4_ysnj.workflow soma-workflow starting in light mode ** Workflow status OK Workflow controller initialised * running Morphologist... * finished. * Run Morphologist_Capsul CNN sulci recognition _Process **Morphologist CAPSUL iteration** started on 2025/07/28 04:43_ progress: 0.0 % ... progress: 100.0 % ... jobs: 4 real, 4 total including barriers _Process **Morphologist CAPSUL iteration** finished on 2025/07/28 04:43 (0 seconds)_ ** Workflow status OK Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.1 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.3 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.3 Warning: wrong filename_base in graph, trying to fix it ok workflow: /tmp/axon_test_qz0fz4xi/tmp/bv_xq4_ysnj.workflow * running CNN... * finished. ** No failed jobs. del WorkflowController ** all OK. ---------------------------------------------------------------------- Ran 1 test in 911.391s OK RETURNCODE: True Exception ignored in: <function TemporaryDirectory.__del__ at 0x737f285380d0> Traceback (most recent call last): File "/casa/install/python/brainvisa/data/neuroDiskItems.py", line 2699, in __del__ TypeError: 'NoneType' object is not callable ================================================================================ SUCCESS (exit code 0) Finished: SUCCESS